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I'm sure you've thought about moving the renderer clientside in JS - what's blocking it? Have you played with ClojureScript before?

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It's certainly crossed my mind, and it'd be great to implement something like that, but the Clojure is just a wrapper around a large and complicated cheminformatics toolkit. Porting the actual rendering library (Java/C++?) would probably be a substantial undertaking.

If it's pure java, it's possible to compile using GWT to JavaScript for use on the client side.

If it's C++, then emscripten might be a possible choice.

If it's a mixture, then that's a much harder problem...

It's probably a hard one:

https://github.com/cryos/avogadro/

Mostly C++, then the clojure wrappers in java? There do exist pure javascript molecule drawers, though.

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